Characterizing protein motions from structure

Journal of Molecular Graphics and Modelling

Volumn 31, Issue , 2011, Pages 41-56

  David, Charles C ^a   Jacobs, Donald J ^b  

^a University of North Carolina at Charlotte   (United States)

^b UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

Essential dynamics; Geometric simulation; Protein flexibility; Subspace comparisons

Indexed keywords

ANISOTROPIC NETWORKS; CLUSTER DECOMPOSITION; COMPARATIVE STUDIES; CONFORMATIONAL ENSEMBLE; DISTANCE CONSTRAINTS; ELASTIC NETWORK MODELS; ESSENTIAL DYNAMICS; GEOMETRIC SIMULATION; KEY DETERMINANTS; MOLECULAR DYNAMICS SIMULATIONS; NATIVE STATE; PARAMETER SETTING; PROTEIN DATA BANK; PROTEIN DYNAMICS; PROTEIN FLEXIBILITY; PROTEIN MOTION; QUANTITATIVE COMPARISON; SINGLE-DOMAIN PROTEINS; SUBSPACE COMPARISONS; THREE MODELS;

DYNAMICS; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PROTEINS;

COMPUTER SIMULATION;

MYOGLOBIN;

ARTICLE; CONTROLLED STUDY; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN STRUCTURE;

ALGORITHMS; ANISOTROPY; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MYOGLOBIN; PRINCIPAL COMPONENT ANALYSIS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 80053903522     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.08.004     Document Type: Article

References (41)

1. F.C. Bernstein, T.F. Koetzle, G.J. Williams, E.E. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi The Protein Data Bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535
2. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N.B.H. Weissig, I.N. Shindyalov, and P.E. Bourne The protein data bank Nucl. Acids Res. 28 2000 235 242 (PubMed: 10592235) (Pubitemid 30047768)
3. J.A. McCammon, B.R. Gelin, and M. Karplus Dynamics of folded proteins Nature 267 1997 585 590 (PubMed: 301613)
4. M.A. Balsera, W. Wriggers, Y. Oono, and K. Schulten Principal component analysis and long time protein dynamics J. Phys. Chem. 100 1996 2567 2572 (Pubitemid 126793208)
5. I. Bahar, A.R. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential Folding Des. 2 1997 173 181 (Pubitemid 127740467)
6. A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, and I. Bahar Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 80 2001 505 515 (PubMed: 11159421)
7. M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 77 1996 1905 1908 (PubMed: 10063201) (Pubitemid 126625816)
8. J. Hub, and B. de Groot Detection of functional modes in protein dynamics PLoS Comput. Biol. 5 2009 e1000480
9. W.G. Krebs, V. Alexandrov, C.A. Wilson, N. Echols, H. Yu, and M. Gerstein Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins 48 2002 682 695 (PubMed: 12211036) (Pubitemid 34925457)
10. I. Bahar, T.R. Lezon, L. Yang, and E. Eyal Global dynamics of proteins: bridging between structure and function 39 2010 23 42
11. D.J. Jacobs, A.J. Rader, L.A. Kuhn, and M.F. Thorpe Protein flexibility predictions using graph theory Proteins: Struct. Funct. Gen. 44 2001 150 165
12. S.A. Wells, S. Menor, B.M. Hespenheide, and M.F. Thorpe Constrained geometric simulation of diffusive motion in proteins Phys. Biol. 2 2005 S127 S136 (Pubitemid 41609439)
13. D.W. Farrell, S. Kirill, and M.F. Thorpe Generating stereochemically acceptable protein pathways Proteins 78 2010 2908 2921
14. S.A. Wells, J.E. Jimenez-Roldan, and R.A. Römer Comparative analysis of rigidity across protein families Phys. Biol. 6 2009 046005 10.1088/1478-3975/6/4/046005
15. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
16. M.W. Van der Kamp, R.D. Schaeffer, A.L. Jonsson, A.D. Scouras, A.M. Simms, R.D. Toofanny, N.C. Benson, P.C. Anderson, E.D. Merkley, S. Rysavy, D. Bromley, D.A.C. Beck, and V. Daggett Dynameomics: a comprehensive database of protein dynamics Structure 18 2010 423 435
17. H.J. Berendsen, and S. Hayward Collective protein dynamics in relation to function Curr. Opin. Struct. Biol. 10 2000 165 169 (Pubitemid 30198942)
18. T.F. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6 (PubMed: 11287673)
19. L. Yang, G. Song, A. Carriquiry, and R.L. Jernigan Close Correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes Structure 16 2008 321 330 (Pubitemid 351215213)
20. A. Amadei, M.A. Ceruso, and A. Di Nola On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations Proteins 36 1999 419 424 (PubMed: 10450083) (Pubitemid 29387740)
21. A. Leo-Macias, P. Lopez-Romero, D. Lupyan, D. Zerbino, and A.R. Ortiz An analysis of core deformations in protein superfamilies Biophys. J. 88 2005 1291 1299 (PubMed: 15542556) (Pubitemid 40975956)
22. J. Miao, and A. Ben-Israel On Principal Angles between Subspaces Lin. Algeb. Appl. 171 1992 81 98
23. H. Gunawan, O. Neswan, and W. Setya-Budhi A formula for angles between subspaces of inner product spaces Contrib. Algeb. Geom. 46 2 2005 311 320 (Pubitemid 43088299)
24. J. Vojtechovsky, K. Chu, J. Berendzen, R.M. Sweet, and I. Schlichting Crystal structures of myoglobin-ligand complexes at near-atomic resolution Biophys. J. 77 1999 2153 2174 (Pubitemid 29463176)
25. S. Fong, S.J. Hamill, M. Proctor, S.M. Freund, G.M. Benian, C. Chothia, M. Bycroft, and J. Clarke Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans J. Mol. Biol. 264 1996 624 639 (Pubitemid 27010748)
26. S. Vijay-Kumar, C.E. Bugg, and W.J. Cook Structure of ubiquitin refined at 1.8 A resolution J. Mol. Biol. 194 1987 531 544
27. E. Lolis, T. Alber, R.C. Davenport, D. Rose, F.C. Hartman, and G.A. Petsko Structure of yeast triosephosphate isomerase at 1.9-A resolution Biochemistry 29 1990 6609 6618 (Pubitemid 20223555)
28. S. Radestock, and H. Gohlke Exploiting the link between protein rigidity and thermostability for data-driven protein engineering Eng. Life Sci. 8 2008 507 522
29. A. Ahmed, S. Villinger, and H. Gohlke Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses Proteins 78 2010 3341 3352
30. K. Pearson On lines and planes of closest fit to systems of points in space Lond. Edinbur. Dublin Philos. Magz. J. Sci. 2 1901 572
31. H. Hotelling Analysis of a complex of statistical variables into principal components J. Edu. Psychol. 24 1933 441
32. B. Manly Multivariate Statistics - A Primer 1986 Chapman & Hall/CRC Boca Raton
33. A. Amadei, A.B. Linssen, and H.J. Berendsen Essential dynamics of proteins Proteins 17 1993 412 425 (PubMed: 8108382) (Pubitemid 23358549)
34. A. Amadei, A.B. Linssen, B.L. de Groot, D.M. van Aalten, and H.J. Berendsen An efficient method for sampling the essential subspace of proteins J. Biomol. Struct. Dyn. 13 1996 615 625 (PubMed: 8906882) (Pubitemid 26081108)
35. D.R. Livesay, S. Dallakyan, G.G. Wood, and D.J. Jacobs A flexible approach for understanding protein stability FEBS Lett. 576 2004 468 476 (Pubitemid 39388647)
36. D.J. Jacobs, D.R. Livesay, J. Hules, and M.L. Tasayco Elucidating quantitative stability-flexibility relationships within thioredoxin and its fragments using a distance constraint model J. Mol. Biol. 358 2006 882 904
37. D.R. Livesay, D.H. Huynh, S. Dallakyan, and D.J. Jacobs Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family Chem. Cent. J. 2 17 2008 1 20
38. P.A. Absil, A. Edelman, and P. Koev On the largest principal angle between random subspaces Lin. Algeb. Appl. 414 1 2006 288 294 (Pubitemid 43276499)
39. M. Zelditch, D. Swiderski, H.D. Sheets, and W. Fink Geometric Morphometrics for Biologists: A primer 2004 Elsevier Academic Press San Diego
40. M. Sun, M.B. Rose, S.K. Ananthanarayanan, D.J. Jacobs, and C.M. Yengo Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle Proc. Natl. Acad. Sci. U. S. A. 105 2008 8631 8636 (Pubitemid 351987731)
41. D.J. Jacobs, D. Trivedi, C. David, and C.M. Yengo Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle J. Mol. Biol. 407 5 2011 Apr 15 716 730 (Epub 2011 Feb 17)